Seurat Analysis
Issei Tsuchiya
19/11/04 22:51
1 Description
This is an R Markdown document for Seurat Analysis. For more details on using R Markdown see http://rmarkdown.rstudio.com.
2 Loading the Dataset
You have chosen
- mca as your library
- GSM2906472_Stomach_dge.txt as 10X directory or count matrix
- MCA_stomach as your project name
- MCA_stomach_FA.rds as output file name.
The output below shows the number of features and samples BEFORE quality control.
## An object of class Seurat
## 14540 features across 3509 samples within 1 assay
## Active assay: RNA (14540 features)3 Quality Control
The figure below shows violin plot and scatter plot for data before the quality control. From this figure, you should decide the parameters for quality control such as maximum percent.mt and minimum nFeature_RNA.
01-VlnPlot.png
## png
## 2
02-ScatterPlot.png
## png
## 2You have chosen
- 50 as
nFeature_RNA_min - 2500 as
nFeature_RNA_max - 50 as
nCount_RNA_min - 10000 as
nCount_RNA_max - 60 as
percent.mt_max.
The output below shows the number of features and samples AFTER quality control.
## An object of class Seurat
## 14540 features across 3474 samples within 1 assay
## Active assay: RNA (14540 features)4 Normalization
The figures below show a subset of features that exhibit high cell-to-cell variation in the dataset. This subset (includes 2000 features) will be used in downstream analysis.
## Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
## Please use `as_label()` or `as_name()` instead.
## This warning is displayed once per session.
03-VariableFeaturePlot.png
## png
## 25 Scaling and Linear Dimensional Reduction
The figures below show the result of scaling and PCA.
## PC_ 1
## Positive: Kcne2, 1810010D01Rik, Slc25a4, Tnni3, Cox7a1
## Negative: Gsta1, Dpcr1, 2210407C18Rik, Krt19, Sptssb
## PC_ 2
## Positive: Cox6a1, Ctse, Cox6b1, Cox7b, Cox7c
## Negative: Igfbp7, Sparc, Col1a2, Col3a1, Vim
## PC_ 3
## Positive: Gm3776, Mgst2, Mal, Cyp2c65, Actg1
## Negative: Pla2g1b, Pgc, mt-Nd1, Clps, mt-Nd4
## PC_ 4
## Positive: 2210407C18Rik, Fabp3, Apoa1, 1810010D01Rik, Lpl
## Negative: Tuba1b, Ube2c, Tff2, Stmn1, Birc5
## PC_ 5
## Positive: Tff2, Ube2c, Birc5, Col1a2, Col3a1
## Negative: Cpe, Chgb, Pcsk2, Resp18, Scg5
04-VizDimLoadings.png
## png
## 2
05-DimPlot.png
## png
## 2
06-DimHeatmap.png
## png
## 2
07-DimHeatmap_mul.png
## png
## 26 Determining the Dimensionality of the Dataset
From the figure below, you should determine significant PCs.
## Warning: Removed 28529 rows containing missing values (geom_point).
08-ElbowPlot.png
## Warning: Removed 28529 rows containing missing values (geom_point).## png
## 2
09-ElbowPlot.png
## png
## 27 Clustering and Non-linear Dimensional Reduction
You have chosen 20 as maximum PC. The figure below shows the result of UMAP / tSNE.
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 3474
## Number of edges: 130680
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8342
## Number of communities: 16
## Elapsed time: 3 seconds## Stomach_1.CCAGACAAGTACGAGATC Stomach_1.GCGTCCACGTTGGTCGGT
## 13 13
## Stomach_1.CCTTTCTCGTAATCGGGT Stomach_1.AACCTACAACAATCACTT
## 13 13
## Stomach_1.AAGCGGCCTTTCGGCTGC
## 6
## Levels: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
10-UMAPPlot.png
## png
## 28 Finding Differentially Expressed Features
The list of differentially expressed features are shown below. This list could be used to assign cell type identity for each cluster.
## # A tibble: 32 x 7
## # Groups: cluster [16]
## p_val avg_logFC pct.1 pct.2 p_val_adj cluster gene
## <dbl> <dbl> <dbl> <dbl> <dbl> <fct> <chr>
## 1 7.02e-213 1.01 0.967 0.92 1.02e-208 0 Pla2g1b
## 2 2.47e- 13 0.754 0.385 0.313 3.59e- 9 0 Sprr1a
## 3 9.51e- 80 0.677 0.884 0.404 1.38e- 75 1 Aldh3a1
## 4 4.17e- 76 0.590 0.867 0.384 6.07e- 72 1 Mogat1
## 5 4.67e-152 1.26 0.748 0.158 6.79e-148 2 Ifrd1
## 6 3.37e-151 1.13 0.748 0.149 4.90e-147 2 Atf3
## 7 1.04e-100 0.530 1 1 1.52e- 96 3 Tff1
## 8 3.69e- 73 0.630 1 0.997 5.36e- 69 3 Gkn2
## 9 3.35e-173 2.08 0.675 0.094 4.87e-169 4 Pga5
## 10 1.61e-143 2.15 1 0.992 2.33e-139 4 Pgc
## # … with 22 more rows8.1 Cluster 0
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Gkn1 5.834622e-284 0.7435286 1.000 1.000 8.483540e-280
## Pla2g1b 7.017638e-213 1.0123723 0.967 0.920 1.020365e-208
## Clps 6.127530e-190 0.4892963 0.984 0.954 8.909429e-186
## Psca 8.860381e-123 0.5751298 0.997 0.989 1.288299e-118
## Txn1 1.246461e-85 -0.7817467 0.162 0.715 1.812354e-81
## Ghrl 3.240990e-79 0.5272985 0.592 0.359 4.712400e-75
## Car2 1.418208e-75 -0.6495360 0.466 0.876 2.062075e-71
## Ppia 2.377941e-72 -0.6841100 0.217 0.748 3.457526e-68
## 1810037I17Rik 1.970698e-71 -0.6430312 0.108 0.575 2.865395e-67
## Rpl9 8.116081e-71 -0.5967535 0.190 0.719 1.180078e-66
## Rpl27 1.678540e-70 -0.6275790 0.193 0.717 2.440598e-66
## Rpl24 1.699913e-69 -0.5776863 0.087 0.528 2.471674e-65
## Ndufa1 4.647717e-68 -0.6120877 0.097 0.540 6.757780e-64
## Hsp90ab1 4.616709e-64 -0.6140068 0.180 0.676 6.712695e-60
## Arf4 4.700751e-64 -0.5644040 0.075 0.481 6.834892e-608.2 Cluster 1
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Gkn2 2.391965e-90 0.5409655 1.000 0.996 3.477917e-86
## Lgals2 3.523127e-87 0.4711213 1.000 0.941 5.122626e-83
## Aldh3a1 9.510956e-80 0.6770368 0.884 0.404 1.382893e-75
## Mogat1 4.174550e-76 0.5896683 0.867 0.384 6.069796e-72
## Mgst3 3.614634e-73 0.5159995 1.000 0.765 5.255678e-69
## Tmsb4x 8.013742e-72 0.3501160 1.000 0.990 1.165198e-67
## Gsta1 1.044180e-70 0.5230200 1.000 0.858 1.518238e-66
## Adh7 2.654264e-68 0.5298974 0.815 0.351 3.859300e-64
## Nqo1 2.563786e-63 0.5302935 0.918 0.457 3.727745e-59
## Pla2g1b 2.973106e-63 -1.7383464 0.939 0.927 4.322896e-59
## Gsta2 3.089962e-60 0.5128346 0.547 0.195 4.492805e-56
## Gsdma2 3.416304e-60 0.5230357 0.962 0.557 4.967306e-56
## Cbr3 9.944070e-58 0.5086896 0.615 0.248 1.445868e-53
## Akr1c19 1.342378e-56 0.4055000 0.528 0.189 1.951818e-52
## Gsta3 4.552514e-55 0.4813645 0.598 0.237 6.619355e-518.3 Cluster 2
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Ifrd1 4.670350e-152 1.2551834 0.748 0.158 6.790690e-148
## Atf3 3.370519e-151 1.1287740 0.748 0.149 4.900734e-147
## Dnajb1 2.205224e-114 1.1093800 0.858 0.316 3.206395e-110
## Klf6 9.177430e-114 0.9412245 0.633 0.140 1.334398e-109
## Ier3 2.358062e-108 0.8997919 0.592 0.125 3.428623e-104
## Zfp36 1.892618e-101 0.8455687 0.685 0.184 2.751867e-97
## Nfkbia 1.752485e-100 0.9830152 0.616 0.154 2.548113e-96
## Areg 1.185916e-99 0.8625652 0.405 0.059 1.724321e-95
## Btg2 1.069351e-98 0.9726077 0.726 0.221 1.554837e-94
## Sfn 1.216227e-97 0.9554750 0.679 0.192 1.768394e-93
## Maff 1.419604e-89 0.7215712 0.362 0.051 2.064104e-85
## Zfand5 2.098083e-85 0.7558631 0.468 0.095 3.050613e-81
## H3f3b 2.049665e-75 0.7206564 0.973 0.754 2.980213e-71
## Errfi1 5.534808e-75 0.6221528 0.323 0.049 8.047612e-71
## Krt8 9.309093e-74 0.5351965 0.995 0.924 1.353542e-698.4 Cluster 3
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Tff1 1.044806e-100 0.5298750 1.000 1.000 1.519147e-96
## Gkn2 3.686806e-73 0.6298872 1.000 0.997 5.360616e-69
## Gkn1 4.322604e-25 0.2752595 1.000 1.000 6.285066e-21
## Gsta1 1.596023e-21 0.3627302 0.982 0.870 2.320617e-17
## Pla2g1b 2.780446e-19 -1.3849175 0.791 0.941 4.042769e-15
## Lgals2 8.668870e-19 0.3069280 0.996 0.946 1.260454e-14
## Fos 5.436481e-17 -0.8559697 0.174 0.444 7.904643e-13
## Ubc 6.056312e-17 -0.7199254 0.262 0.541 8.805878e-13
## Mgst3 1.111019e-16 0.3324733 0.961 0.786 1.615422e-12
## Hsp90aa1 4.226800e-15 -0.7380539 0.163 0.425 6.145767e-11
## Dnajb1 3.017661e-14 -0.9935968 0.163 0.391 4.387679e-10
## Hspa1a 6.379185e-14 -0.7918818 0.124 0.355 9.275336e-10
## Ier2 1.871885e-12 -0.5683527 0.089 0.297 2.721721e-08
## Sptssb 5.859878e-12 0.3318405 0.851 0.651 8.520262e-08
## Pdlim1 3.115265e-11 -0.6360393 0.078 0.263 4.529596e-078.5 Cluster 4
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Pga5 3.348012e-173 2.0818119 0.675 0.094 4.868009e-169
## Pgc 1.605181e-143 2.1475280 1.000 0.992 2.333934e-139
## Muc6 3.199077e-121 1.5321825 0.394 0.036 4.651458e-117
## Tstd1 9.064977e-115 1.4772478 0.635 0.137 1.318048e-110
## Psca 1.153110e-106 -1.4048496 0.949 0.994 1.676621e-102
## Gkn2 7.249260e-105 -1.8686570 0.993 0.997 1.054042e-100
## A4gnt 3.010350e-104 1.2339466 0.347 0.033 4.377049e-100
## Gkn1 1.027964e-102 -1.2025608 1.000 1.000 1.494660e-98
## Tff1 5.544897e-102 -1.3063453 1.000 1.000 8.062280e-98
## Agr2 2.566888e-91 1.1364336 0.985 0.828 3.732256e-87
## Gsta1 7.053360e-90 -1.9218254 0.602 0.903 1.025558e-85
## Creb3l4 6.360726e-88 0.9851435 0.307 0.031 9.248496e-84
## Cfi 1.199434e-81 1.5312972 0.628 0.197 1.743977e-77
## Bex4 4.055678e-72 0.9485392 0.255 0.026 5.896955e-68
## Krt19 1.735393e-71 -1.2198483 0.682 0.896 2.523261e-678.6 Cluster 5
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Gm23935 3.577144e-179 3.1225846 0.904 0.262 5.201167e-175
## Gm26917 8.176501e-154 3.4071532 0.904 0.346 1.188863e-149
## Gm42418 1.585654e-149 2.9562911 0.952 0.510 2.305540e-145
## mt-Cytb 2.684246e-119 0.9433085 1.000 0.997 3.902894e-115
## Lars2 2.778163e-113 1.8151120 0.357 0.033 4.039449e-109
## mt-Co1 1.418196e-112 0.8325202 1.000 0.999 2.062058e-108
## mt-Nd1 2.343701e-110 0.8354652 1.000 1.000 3.407741e-106
## mt-Nd4 1.575383e-101 0.8075484 1.000 0.994 2.290607e-97
## mt-Nd2 6.039149e-84 0.7525960 0.996 0.972 8.780923e-80
## Slc25a5 1.405658e-69 -0.9078609 0.636 0.940 2.043827e-65
## Ftl1 1.347734e-66 -1.0727143 0.463 0.878 1.959606e-62
## mt-Nd3 4.832404e-57 0.8543032 0.949 0.857 7.026316e-53
## Calm1 1.754656e-49 -0.8369529 0.544 0.866 2.551270e-45
## mt-Nd5 1.995694e-46 0.6712232 0.974 0.904 2.901738e-42
## Cox6b1 4.971354e-45 -0.8000391 0.507 0.887 7.228349e-418.7 Cluster 6
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Krt7 5.427993e-147 1.1138507 0.455 0.033 7.892302e-143
## S100a10 3.644044e-136 1.1275526 0.532 0.055 5.298439e-132
## Clca1 1.531815e-135 1.3579613 0.300 0.011 2.227259e-131
## Krt20 9.086730e-120 1.4891010 0.395 0.032 1.321211e-115
## Gpa33 3.789409e-105 0.8499814 0.313 0.021 5.509800e-101
## Rbp1 3.176833e-103 1.3357134 0.562 0.090 4.619115e-99
## Anxa2 9.690251e-96 1.2283537 0.815 0.244 1.408963e-91
## Fabp2 8.938581e-94 1.4914049 0.708 0.181 1.299670e-89
## Pdlim1 5.388418e-90 1.2351379 0.751 0.212 7.834759e-86
## Gstm3 2.003103e-88 1.1419628 0.476 0.074 2.912511e-84
## Lgals4 3.732228e-86 1.3214595 0.884 0.363 5.426660e-82
## Akr1b8 1.036088e-78 1.0338908 0.571 0.122 1.506472e-74
## S100a6 1.382268e-78 1.2047904 0.983 0.752 2.009818e-74
## S100a14 1.750184e-78 0.8273095 0.378 0.050 2.544768e-74
## Dmbt1 1.949927e-73 1.0663237 0.429 0.069 2.835194e-698.8 Cluster 7
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Kcne2 0.000000e+00 1.6642299 0.608 0.014 0.000000e+00
## Igfbp2 6.719875e-283 1.4957356 0.498 0.009 9.770699e-279
## Tnni3 2.448050e-279 1.9687220 0.696 0.037 3.559464e-275
## 1810010D01Rik 1.914803e-270 2.8719327 0.912 0.108 2.784124e-266
## Cox7a1 1.385273e-258 2.0817628 0.784 0.065 2.014187e-254
## Hamp2 3.704372e-254 2.4131786 0.744 0.057 5.386158e-250
## Ckb 6.684357e-241 1.8713014 0.775 0.066 9.719055e-237
## Fabp3 1.155497e-236 2.1772580 0.811 0.085 1.680093e-232
## Fabp12 2.047568e-234 1.0750641 0.401 0.006 2.977164e-230
## Apoa4 2.334622e-204 0.9693374 0.339 0.004 3.394540e-200
## Slc26a9 9.424181e-195 1.0492774 0.436 0.016 1.370276e-190
## Atp4a 7.248993e-189 2.9165744 0.960 0.248 1.054004e-184
## Glod5 2.498152e-188 1.2471050 0.511 0.030 3.632313e-184
## Apoa1 6.947210e-184 3.0521440 0.965 0.256 1.010124e-179
## Gga2 4.264900e-180 1.1350282 0.454 0.023 6.201165e-1768.9 Cluster 8
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Birc5 1.304418e-307 1.4634678 0.653 0.020 1.896624e-303
## Ube2c 4.001223e-262 1.6490295 0.638 0.028 5.817778e-258
## Ccna2 8.799713e-249 1.0593419 0.437 0.007 1.279478e-244
## Stmn1 4.523567e-225 1.5081790 0.739 0.056 6.577267e-221
## Pclaf 1.512602e-222 1.2646397 0.513 0.019 2.199323e-218
## Cdca3 6.542137e-198 1.0279231 0.452 0.016 9.512267e-194
## Cdk1 1.401522e-196 0.9147094 0.382 0.009 2.037814e-192
## Ccnb1 4.174912e-173 0.9006089 0.307 0.005 6.070322e-169
## Tk1 1.669722e-169 0.9281937 0.412 0.017 2.427776e-165
## Spc24 2.476940e-166 1.0550353 0.457 0.024 3.601471e-162
## Cdc20 3.378778e-158 0.8953592 0.296 0.006 4.912744e-154
## Tuba1b 2.226507e-156 1.7135006 0.809 0.127 3.237341e-152
## Cenpa 1.276602e-147 0.9584450 0.337 0.012 1.856179e-143
## Cdca8 5.404025e-147 0.8019275 0.357 0.014 7.857452e-143
## Ccnb2 4.283088e-142 0.8554981 0.327 0.012 6.227609e-1388.10 Cluster 9
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Hsd17b2 2.006127e-75 0.9126291 0.442 0.055 2.916909e-71
## Mgll 3.591030e-74 0.8974862 0.436 0.054 5.221357e-70
## Rep15 2.061425e-65 1.0079266 0.750 0.189 2.997312e-61
## 2210407C18Rik 3.129180e-64 1.0232586 1.000 0.815 4.549827e-60
## Lypd8 1.053758e-63 1.3353932 0.968 0.408 1.532165e-59
## Rnase4 1.816138e-63 1.0492192 0.647 0.143 2.640665e-59
## Ces2c 1.801622e-57 0.8637546 0.538 0.107 2.619559e-53
## Sectm1b 4.579220e-57 0.9313673 0.583 0.128 6.658186e-53
## Cdkn1a 7.832693e-54 0.8994625 0.718 0.197 1.138874e-49
## Ctse 9.508335e-54 0.8830711 1.000 0.679 1.382512e-49
## AA467197 4.218632e-53 0.8390324 0.551 0.117 6.133891e-49
## Gsta1 7.654728e-52 0.7689588 1.000 0.873 1.112997e-47
## Mal 1.326133e-51 0.9575847 0.904 0.358 1.928197e-47
## Fhl1 2.610769e-50 0.8827660 0.756 0.231 3.796057e-46
## Psca 3.543829e-50 0.6119393 1.000 0.990 5.152728e-468.11 Cluster 10
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Vim 0.000000e+00 2.592415 0.594 0.001 0.000000e+00
## Igfbp7 2.035494e-257 3.421437 0.551 0.007 2.959608e-253
## Col1a2 3.058808e-252 3.125029 0.464 0.004 4.447507e-248
## Col3a1 7.914411e-237 2.959682 0.449 0.004 1.150755e-232
## C1s1 1.168453e-228 1.533967 0.304 0.000 1.698930e-224
## Dpt 4.854974e-226 2.329031 0.362 0.001 7.059132e-222
## Bgn 4.063912e-222 2.349416 0.420 0.004 5.908929e-218
## Tgfbi 2.600395e-219 1.940979 0.319 0.001 3.780974e-215
## Col6a1 3.918576e-218 1.957259 0.304 0.000 5.697609e-214
## Postn 1.534401e-215 2.518132 0.348 0.001 2.231019e-211
## Ly6a 3.505807e-193 2.493357 0.420 0.005 5.097444e-189
## Rarres2 6.155455e-191 2.068920 0.333 0.002 8.950032e-187
## Mxra8 8.856066e-187 1.515949 0.275 0.001 1.287672e-182
## Sparc 1.473318e-182 3.884966 0.609 0.019 2.142204e-178
## Emp3 1.600232e-178 1.809340 0.391 0.005 2.326737e-1748.12 Cluster 11
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Chgb 0.000000e+00 3.522201 0.887 0.008 0.000000e+00
## Pcsk2 0.000000e+00 3.066393 0.755 0.006 0.000000e+00
## Resp18 0.000000e+00 3.024242 0.774 0.007 0.000000e+00
## Scg5 0.000000e+00 2.639698 0.717 0.006 0.000000e+00
## Pcsk1 5.736159e-278 1.725249 0.434 0.001 8.340375e-274
## Pnoc 1.067325e-263 2.158669 0.415 0.001 1.551891e-259
## Tm4sf4 5.431781e-258 1.746036 0.377 0.001 7.897810e-254
## Pcsk1n 2.410015e-257 2.285868 0.509 0.004 3.504162e-253
## Fam183b 3.018361e-250 1.630978 0.434 0.002 4.388697e-246
## Cpe 4.038447e-246 3.710660 0.849 0.022 5.871902e-242
## Mrln 4.453570e-236 1.602094 0.377 0.001 6.475490e-232
## Hap1 4.380017e-215 1.624137 0.396 0.002 6.368545e-211
## Scg3 5.891213e-205 1.403121 0.321 0.001 8.565823e-201
## Chga 1.740856e-194 3.454803 0.585 0.011 2.531205e-190
## Rbp4 1.329830e-193 2.322627 0.491 0.007 1.933573e-1898.13 Cluster 12
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Isg15 2.187055e-250 2.1429401 0.750 0.014 3.179979e-246
## Oasl2 1.829799e-186 1.2927125 0.615 0.013 2.660528e-182
## Ifit1 1.594254e-177 1.2462240 0.269 0.001 2.318045e-173
## Igtp 2.033744e-103 1.0126679 0.288 0.005 2.957064e-99
## Bst2 1.057173e-90 1.3804263 0.596 0.034 1.537130e-86
## Ifih1 9.247555e-80 0.6437471 0.308 0.008 1.344595e-75
## Psmb8 2.452663e-77 0.8696282 0.327 0.010 3.566173e-73
## Oas1a 1.042919e-73 1.0868185 0.577 0.039 1.516404e-69
## Irf7 1.010543e-71 1.2330440 0.462 0.025 1.469330e-67
## Rtp4 9.771428e-63 1.0092662 0.288 0.010 1.420766e-58
## Stat1 2.027288e-34 0.7456908 0.308 0.024 2.947676e-30
## Cd74 1.672796e-33 0.6988904 0.269 0.019 2.432245e-29
## AW112010 3.674412e-29 1.4081128 0.481 0.072 5.342595e-25
## Lypd8 8.635484e-27 1.8897851 0.962 0.425 1.255599e-22
## B2m 4.464688e-25 1.4043240 0.923 0.382 6.491657e-218.14 Cluster 13
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Try10 1.157410e-244 1.8891877 0.459 0.002 1.682874e-240
## Try4 1.967400e-104 2.4191559 0.378 0.007 2.860600e-100
## Gif 1.735543e-89 3.6192492 1.000 0.088 2.523479e-85
## Furin 3.605310e-72 1.9090808 0.486 0.021 5.242120e-68
## Chia1 9.942700e-39 4.5919771 0.973 0.245 1.445669e-34
## Tmed6 3.346438e-38 2.7383626 0.676 0.093 4.865722e-34
## Pdia2 2.052446e-33 1.8922693 0.568 0.070 2.984256e-29
## Pnliprp2 2.606213e-31 1.6864126 0.351 0.027 3.789433e-27
## Nupr1 1.054439e-29 1.7899015 0.541 0.068 1.533154e-25
## Pla2g1b 1.124461e-25 3.3310525 1.000 0.928 1.634966e-21
## Clps 1.214622e-25 3.5986804 1.000 0.959 1.766060e-21
## Pgc 9.289057e-23 1.9385822 1.000 0.992 1.350629e-18
## Tmsb4x 6.092379e-19 -1.3834447 0.892 0.992 8.858320e-15
## Gsta4 1.871862e-15 -1.6489358 0.378 0.908 2.721687e-11
## mt-Co1 6.041881e-15 -0.8115644 0.973 0.999 8.784895e-118.15 Cluster 14
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Cldn2 1.852184e-242 1.4451376 0.528 0.003 2.693075e-238
## Aqp5 9.670231e-181 2.2865148 0.722 0.015 1.406052e-176
## Kcne3 8.328407e-133 2.5739196 0.889 0.038 1.210950e-128
## Wfdc18 3.820056e-104 0.9598366 0.278 0.003 5.554362e-100
## Pigr 6.703236e-91 1.5485343 0.583 0.022 9.746506e-87
## Klk1 1.450981e-50 1.8592600 0.722 0.071 2.109727e-46
## Cldn7 5.823288e-50 0.8969914 0.333 0.013 8.467060e-46
## Muc6 3.912178e-46 1.7602434 0.639 0.058 5.688307e-42
## Cd44 2.728295e-45 1.1301693 0.306 0.013 3.966942e-41
## Cela1 3.717904e-39 2.9635020 1.000 0.250 5.405832e-35
## Sord 4.397858e-38 1.1147528 0.361 0.022 6.394485e-34
## Rbp1 2.766194e-36 1.6954344 0.778 0.115 4.022046e-32
## Spp1 3.452239e-36 2.5246215 0.750 0.115 5.019556e-32
## Cpn1 6.650333e-36 1.2681747 0.556 0.056 9.669584e-32
## Hgfac 1.634263e-33 0.9580063 0.417 0.033 2.376219e-298.16 Cluster 15
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Sh2d6 0.000000e+00 2.982184 0.815 0.004 0.000000e+00
## Lrmp 0.000000e+00 2.891251 0.889 0.005 0.000000e+00
## Alox5ap 0.000000e+00 2.781436 0.889 0.008 0.000000e+00
## Hck 0.000000e+00 2.715583 0.852 0.002 0.000000e+00
## Rgs13 0.000000e+00 2.681779 0.741 0.003 0.000000e+00
## Alox5 0.000000e+00 2.539026 0.815 0.001 0.000000e+00
## Dclk1 0.000000e+00 2.457819 0.815 0.003 0.000000e+00
## Spib 0.000000e+00 1.971029 0.630 0.002 0.000000e+00
## Cdhr2 2.560642e-278 1.887951 0.481 0.001 3.723174e-274
## Trpm5 7.341159e-274 2.028558 0.519 0.002 1.067405e-269
## Strip2 1.645496e-260 1.508359 0.407 0.001 2.392552e-256
## Gng13 1.178249e-231 2.412228 0.667 0.006 1.713174e-227
## Rac2 1.700144e-229 1.906334 0.593 0.004 2.472010e-225
## Sh2d7 1.143929e-225 1.505336 0.407 0.001 1.663273e-221
## Nrgn 1.422247e-225 1.872588 0.407 0.001 2.067947e-2219 Plotting Features
11-Interested_VlnPlot.png
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12-Interested_FeaturePlot.png
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13-Top10Marker_Heatmap.png
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